/ 
bioperl-run-1.5.2_100
/ Bio::Tools::Run::PiseApplication::treealign

NAME

Bio::Tools::Run::PiseApplication::treealign

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::treealign

      Bioperl class for:

	treealign	phylogenetic alignment of homologous sequences (J. Hein)

	References:

		Hein, J.: Unified approach to alignment and phylogenies. Meth. Enzymol. 183:626-645 (1990).

		Hein, J.: A new method that simultaneously aligns and reconstruct ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-668 (1989). 

		Hein, J.: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6:669-684 (1989). 



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/treealign.html 
         for available values):


		treealign (String)

		fileseq (Sequence)
			Sequences File
			pipe: seqsfile

		seqtype (Excl)
			Sequence type

		nuseq (Integer)
			Number of sequences

		gap_open (Integer)
			Gap open penalty

		gap_ext (Integer)
			Gap extension penalty

		ancesterout (Switch)
			Present ancestral sequences

		usertree (Switch)
			User tree

		usertreefile (InFile)
			Your tree file

		filetree (OutFile)

		fileali (OutFile)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

  • http://bioweb.pasteur.fr/seqanal/interfaces/treealign.html

  • Bio::Tools::Run::PiseApplication

  • Bio::Tools::Run::AnalysisFactory::Pise

  • Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $treealign = Bio::Tools::Run::PiseApplication::treealign->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::treealign object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $treealign = $factory->program('treealign');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::treealign.